Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1696 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0805944879 sf0805943882 8 5944879 7.78E-14 1.25E-07
vg0623849092 sf0623848095 6 23849092 4.68E-13 NA
vg0626755903 sf0626754906 6 26755903 5.79E-13 NA
vg0202777372 sf0202777370 2 2777372 8.85E-13 5.84E-07
vg0218843921 sf0218838052 2 18843921 1.38E-12 NA
vg1002756136 sf1002755113 10 2756136 2.25E-12 4.67E-06
vg0626773622 sf0626772625 6 26773622 2.81E-12 NA
vg0321376438 sf0321374948 3 21376438 9.59E-12 1.80E-06
vg1214334991 sf1214332331 12 14334991 8.25E-10 3.32E-06
vg0626921887 sf0626920890 6 26921887 1.79E-09 1.10E-06
vg1015779989 sf1015708759 10 15779989 2.80E-08 6.12E-06
vg0233663282 sf0233657413 2 33663282 2.47E-07 4.67E-06
vg1214616166 sf1214613506 12 14616166 NA 4.09E-07
vg0223422604 sf0223416735 2 23422604 NA 7.30E-07